I broke this OP and its replies out and put it into a separate thread in The Academy, so as not to clutter the 6.30 bugs thread with a discussion of a "Working as intended" (or at least "mostly as intended") feature. In answer to the OP's implied question "Did I put this in the right place?" (hidden behind the spoiler tag), the answer is "We encourage new players to first post things they think are bugs in The Academy to get confirmation that they really are bugs, or to hone in on what the actual bug is before posting to the bugs thread." See the "Where should I post?" FAQ more details.
As to what is going on: All of the ship objects in the code point to a design object (I'm using the computer science term "object" here loosely - in reality they're mostly entries in the database). If you change the properties of the design object, the ship objects change magically to have the properties of the modified design. This is what the "new design" button is for - when you want to modify a design that is in production, you should create a new design and edit that. There are safeguards built into Aurora to keep you from accidentally modifying such a design (such as requiring a design be locked before you put it into production, and requiring SM mode to unlock a locked design) but they can be circumvented by SM mode. (This is intentional so that you can work around bugs or mistakes, as someone already mentioned).
So what presumably happened is that after the OP put the design into production, he used SM mode to unlock the design and modify it. At that point all bets were off - he was intentionally going into expert mode to make a non-realistic change. Assuming that he did have to use SM mode to make the change, then the only thing I can see that might not be working as intended is the fact that the build cost wasn't updated when the design was changed. To put it another way, the OP could have waited until the ship was built, made the change, and seen exactly the same result - an almost free super-ship.
So the big question to the OP is: "Are you absolutely certain you didn't use SM mode anywhere in this process, either to build an unlocked design or to unlock the design after it was in production?" (And by asking that question I just realized what the real issue may be:) If the answer to that is "Yes", then the next question is "Did you use industrial factories to build these things, or shipyards?" If the answer is "shipyards", then something really weird is going on, since this should be well-established code. If the answer is "industrial factories", then there's a good chance that the actual bug is "I'm able to use industrial factories to build a design that isn't frozen."
John